Re: [galaxy-dev] unable to login user to local instance
Peter Cock wrote:
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else content[:length].rsplit('
', 1)[0]+suffix)
^
SyntaxError: invalid syntax
I deduce you're using Python 2.4, since that line of code
is using the ternary operator added in Python 2.5
http://www.python.org/dev/peps/pep-0308/
Now that it has been reported I think it will be fixed to work with
Python 2.4. However, the Galaxy team have indicated they will
be dropping Python 2.4 (probably this year) so if I were you
since this is a new setup I'd install Python 2.6 on this machine
(Galaxy doesn't yet support Python 2.7).
It was actually already fixed in 5019:39b40280ed6d, which was part of
the last stable release.
--nate
Peter
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
Ryan, congratulations on getting this far! Thank you! :) Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser. First issue - When I go to User - Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org http://usegalaxy.org site. Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this? Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ' at the top of the popup, then you are logged in. Otherwise not. yeah, I'm definitely not logged in. Something isn't taking. Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not. No, I haven't done anything with admin stuff yet. Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :) I will, but first I want to get the default install working properly before doing anything else. SOI've removed the Apache proxy and am hitting galaxy directly on localhost:8080. Logging in still doesn't work. What else should I check? I'm connected to a mySQL database running on a different server. Could there be a problem there? paster.log doesn't seem to be much help in debugging this... attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
Ok, I don't know what happened with this...I reinstalled from scratch
and i seems to be working now. I suspect perhaps because I started
galaxy a few times before migrating to mysql. This time, I deleted
everything, changed the config settings then started galaxy.
I'm now on to testing my cluster integration...so, I'm following this:
https://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn
as my initial test. When I run the get flanks, I see the job get
started on the cluster and errors out with the following error:
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py,
line 16, in ?
from galaxy.tools.util.galaxyops import *
File /home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py, line
15, in ?
from galaxy import util, jobs, model
File /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 4, in ?
from galaxy import util, model
File /home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line
11, in ?
import galaxy.datatypes.registry
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py,
line 6, in ?
import data, tabular, interval, images, sequence, qualityscore,
genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py, line 7,
in ?
import metadata
File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py,
line 5, in ?
from galaxy.web import form_builder
File /home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py, line 5, in ?
from framework import expose, json, json_pretty, require_login,
require_admin, url_for, error, form, FormBuilder, expose_api
File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 18, in ?
import helpers
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else
content[:length].rsplit(' ', 1)[0]+suffix)
^
SyntaxError: invalid syntax
If I submit the job script from the shell, the job runs, but when the
web interface submits the job it doesn't. In both cases, its the galaxy
user account so I don't think environment variables are to blame.
On 2/18/11 10:26 AM, Ryan Golhar wrote:
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my
cluster integration tomorrow. For now, I can see galaxy from my web
browser.
First issue - When I go to User - Login and try to log myself in
(I've already registered myself), it looks like it works, but the
browser get redirected really fast to another page, then again to
the main page. The User menu never shows me as logged in as it does
on the public usegalaxy.org http://usegalaxy.org site.
Is there a way to check that I'm actually logged in? If its not
showing, then I assume something is wrong. Where do I look to debug
this?
Try hovering your mouse over the 'User' tab top right of the screen - if
you see 'logged in as ' at the top of the popup, then you are
logged in. Otherwise not.
yeah, I'm definitely not logged in. Something isn't taking.
Also, if you have added your login email to the list of admin_users in
universe_wsgi.ini (and restarted galaxy of course...), then you can tell
you are logged in if you can see an 'Admin' tab - otherwise not.
No, I haven't done anything with admin stuff yet.
Depending on your situation, you may want to consider using external
authentication against (eg) an existing organizational
ldap/active_directory or other authentication database and have apache
pass the authentication headers through to a proxied galaxy. It's not
trivial but the benefit is that users have single sign on - one less
password to forget :)
I will, but first I want to get the default install working properly
before doing anything else.
SOI've removed the Apache proxy and am hitting galaxy directly on
localhost:8080. Logging in still doesn't work. What else should I check?
I'm connected to a mySQL database running on a different server. Could
there be a problem there? paster.log doesn't seem to be much help in
debugging this...
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
--
CONFIDENTIALITY NOTICE: This email communication may contain private,
confidential, or legally privileged information intended for the sole
use of the designated and/or duly authorized recipient(s). If you are
not the intended recipient or have received this email in error, please
notify the sender immediately by email and permanently delete all copies
of this email including all attachments without reading them. If you are
the intended recipient, secure the contents in a manner that conforms to
all applicable state and/or federal requirements related to privacy and
Re: [galaxy-dev] unable to login user to local instance
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golha...@umdnj.edu wrote:
Ok, I don't know what happened with this...I reinstalled from scratch and ...
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py, line
16, in ?
...
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else content[:length].rsplit('
', 1)[0]+suffix)
^
SyntaxError: invalid syntax
I deduce you're using Python 2.4, since that line of code
is using the ternary operator added in Python 2.5
http://www.python.org/dev/peps/pep-0308/
Now that it has been reported I think it will be fixed to work with
Python 2.4. However, the Galaxy team have indicated they will
be dropping Python 2.4 (probably this year) so if I were you
since this is a new setup I'd install Python 2.6 on this machine
(Galaxy doesn't yet support Python 2.7).
Peter
___
To manage your subscriptions to this and other Galaxy lists, please use the
interface at:
http://lists.bx.psu.edu/
[galaxy-dev] unable to login user to local instance
Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser. First issue - When I go to User - Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org site. Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this? ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] unable to login user to local instance
Ryan, congratulations on getting this far! On Fri, Feb 18, 2011 at 3:52 PM, Ryan Golhar golha...@umdnj.edu wrote: Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser. First issue - When I go to User - Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org site. Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this? Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ' at the top of the popup, then you are logged in. Otherwise not. Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not. Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :) ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Ross Lazarus MBBS MPH Associate Professor, HMS; Director of Bioinformatics, Channing Laboratory; 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850 Head, Medical Bioinformatics, BakerIDI; PO Box 6492, St Kilda Rd Central; Melbourne, VIC 8008, Australia; Tel: +61 385321444 ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
